Wave-induced fatigue damage is an important component of deep-water steel catenary riser (SCR) fatigue damage. In this paper, the fatigue damage caused by SCR wave in the South China Sea caused by storm state is predicted through time domain and frequency domain respectively. The difference of platform motion response and riser dynamic response obtained by time domain method and frequency domain method is also analyzed. The prediction results of fatigue damage risk position and damage extreme value are then compared. The applicability of the methods in prediction of deep-ocean risers’ wave-induced fatigue was evaluated. The result show that there is a huge gap between the time domain method and the frequency domain method, and that the damage risk position calculated by the frequency domain method is lagging behind. With the frequency domain method, the wave-induced fatigue cumulative damage is amplified, while the order of magnitude is consistent.